### This is a temporary parameter file made for residue PL9 ###
### Make sure that all the parameters are verified before using this file as a global parameter file ###

CONFLIST PL9        PL9BK PL901 PL9-1

NATOM    PL9BK      41
NATOM    PL901       4
NATOM    PL9-1       4

IATOM    PL9BK  C2     0
IATOM    PL9BK  C3     1
IATOM    PL9BK  C5     2
IATOM    PL9BK  C6     3
IATOM    PL9BK  C7     4
IATOM    PL9BK  C8     5
IATOM    PL9BK  C9     6
IATOM    PL9BK  C10    7
IATOM    PL9BK  C11    8
IATOM    PL9BK  C12    9
IATOM    PL9BK  C13   10
IATOM    PL9BK  C14   11
IATOM    PL9BK  C15   12
IATOM    PL9BK  C16   13
IATOM    PL9BK  C17   14
IATOM    PL9BK  C18   15
IATOM    PL9BK  C19   16
IATOM    PL9BK  C20   17
IATOM    PL9BK  C21   18
IATOM    PL9BK  C22   19
IATOM    PL9BK  C23   20
IATOM    PL9BK  C24   21
IATOM    PL9BK  C25   22
IATOM    PL9BK  C26   23
IATOM    PL9BK  C27   24
IATOM    PL9BK  C28   25
IATOM    PL9BK  C29   26
IATOM    PL9BK  C30   27
IATOM    PL9BK  C31   28
IATOM    PL9BK  C32   29
IATOM    PL9BK  C33   30
IATOM    PL9BK  C34   31
IATOM    PL9BK  C35   32
IATOM    PL9BK  C36   33
IATOM    PL9BK  C37   34
IATOM    PL9BK  C38   35
IATOM    PL9BK  C39   36
IATOM    PL9BK  C40   37
IATOM    PL9BK  C41   38
IATOM    PL9BK  C52   39
IATOM    PL9BK  C53   40

IATOM    PL901  C1    0
IATOM    PL901  O2    1
IATOM    PL901  C4    2
IATOM    PL901  O1    3

IATOM    PL9-1  C1    0
IATOM    PL9-1  O2    1
IATOM    PL9-1  C4    2
IATOM    PL9-1  O1    3

ATOMNAME PL9BK    0  C2 
ATOMNAME PL9BK    1  C3 
ATOMNAME PL9BK    2  C5 
ATOMNAME PL9BK    3  C6 
ATOMNAME PL9BK    4  C7 
ATOMNAME PL9BK    5  C8 
ATOMNAME PL9BK    6  C9 
ATOMNAME PL9BK    7  C10
ATOMNAME PL9BK    8  C11
ATOMNAME PL9BK    9  C12
ATOMNAME PL9BK   10  C13
ATOMNAME PL9BK   11  C14
ATOMNAME PL9BK   12  C15
ATOMNAME PL9BK   13  C16
ATOMNAME PL9BK   14  C17
ATOMNAME PL9BK   15  C18
ATOMNAME PL9BK   16  C19
ATOMNAME PL9BK   17  C20
ATOMNAME PL9BK   18  C21
ATOMNAME PL9BK   19  C22
ATOMNAME PL9BK   20  C23
ATOMNAME PL9BK   21  C24
ATOMNAME PL9BK   22  C25
ATOMNAME PL9BK   23  C26
ATOMNAME PL9BK   24  C27
ATOMNAME PL9BK   25  C28
ATOMNAME PL9BK   26  C29
ATOMNAME PL9BK   27  C30
ATOMNAME PL9BK   28  C31
ATOMNAME PL9BK   29  C32
ATOMNAME PL9BK   30  C33
ATOMNAME PL9BK   31  C34
ATOMNAME PL9BK   32  C35
ATOMNAME PL9BK   33  C36
ATOMNAME PL9BK   34  C37
ATOMNAME PL9BK   35  C38
ATOMNAME PL9BK   36  C39
ATOMNAME PL9BK   37  C40
ATOMNAME PL9BK   38  C41
ATOMNAME PL9BK   39  C52
ATOMNAME PL9BK   40  C53

ATOMNAME PL901    0  C1 
ATOMNAME PL901    1  O2 
ATOMNAME PL901    2  C4 
ATOMNAME PL901    3  O1 

ATOMNAME PL9-1    0  C1 
ATOMNAME PL9-1    1  O2 
ATOMNAME PL9-1    2  C4 
ATOMNAME PL9-1    3  O1 

CONNECT  PL9BK  C2  ion        0    C3   0    C1 
CONNECT  PL9BK  C3  ion        0    C2   0    C4   0    C7 
CONNECT  PL9BK  C5  ion        0    C4   0    C6   0    C52
CONNECT  PL9BK  C6  ion        0    C5   0    C1   0    C53
CONNECT  PL9BK  C7  ion        0    C3   0    C8 
CONNECT  PL9BK  C8  ion        0    C7   0    C9 
CONNECT  PL9BK  C9  ion        0    C8   0    C10  0    C11
CONNECT  PL9BK  C10 ion        0    C9 
CONNECT  PL9BK  C11 ion        0    C9   0    C12
CONNECT  PL9BK  C12 ion        0    C11  0    C13
CONNECT  PL9BK  C13 ion        0    C12  0    C14
CONNECT  PL9BK  C14 ion        0    C13  0    C15  0    C16
CONNECT  PL9BK  C15 ion        0    C14
CONNECT  PL9BK  C16 ion        0    C14  0    C17
CONNECT  PL9BK  C17 ion        0    C16  0    C18
CONNECT  PL9BK  C18 ion        0    C17  0    C19
CONNECT  PL9BK  C19 ion        0    C18  0    C20  0    C21
CONNECT  PL9BK  C20 ion        0    C19
CONNECT  PL9BK  C21 ion        0    C19  0    C22
CONNECT  PL9BK  C22 ion        0    C21  0    C23
CONNECT  PL9BK  C23 ion        0    C22  0    C24
CONNECT  PL9BK  C24 ion        0    C23  0    C25  0    C26
CONNECT  PL9BK  C25 ion        0    C24
CONNECT  PL9BK  C26 ion        0    C24  0    C27
CONNECT  PL9BK  C27 ion        0    C26  0    C28
CONNECT  PL9BK  C28 ion        0    C27  0    C29
CONNECT  PL9BK  C29 ion        0    C28  0    C30  0    C31
CONNECT  PL9BK  C30 ion        0    C29
CONNECT  PL9BK  C31 ion        0    C29  0    C32
CONNECT  PL9BK  C32 ion        0    C31  0    C33
CONNECT  PL9BK  C33 ion        0    C32  0    C34
CONNECT  PL9BK  C34 ion        0    C33  0    C35  0    C36
CONNECT  PL9BK  C35 ion        0    C34
CONNECT  PL9BK  C36 ion        0    C34  0    C37
CONNECT  PL9BK  C37 ion        0    C36  0    C38
CONNECT  PL9BK  C38 ion        0    C37  0    C39
CONNECT  PL9BK  C39 ion        0    C38  0    C40  0    C41
CONNECT  PL9BK  C40 ion        0    C39
CONNECT  PL9BK  C41 ion        0    C39
CONNECT  PL9BK  C52 ion        0    C5 
CONNECT  PL9BK  C53 ion        0    C6 

CONNECT  PL901  C1  ion        0    C2   0    C6   0    O2 
CONNECT  PL901  C4  ion        0    C3   0    C5   0    O1 
CONNECT  PL901  O1  ion        0    C4 
CONNECT  PL901  O2  ion        0    C1 

CONNECT  PL9-1  C1  ion        0    C2   0    C6   0    O2 
CONNECT  PL9-1  C4  ion        0    C3   0    C5   0    O1 
CONNECT  PL9-1  O1  ion        0    C4 
CONNECT  PL9-1  O2  ion        0    C1 

CHARGE   PL901  O2  -0.20            #fake charges
CHARGE   PL901  C1  +0.20
CHARGE   PL901  O1  -0.20
CHARGE   PL901  C4  +0.20

CHARGE   PL9-1  O2  -0.50
CHARGE   PL9-1  C1  -0.00
CHARGE   PL9-1  O1  -0.50
CHARGE   PL9-1  C4  -0.00

PROTON   PL901      0
PKA      PL901      0.0       
ELECTRON PL901      0
EM       PL901      0.0       
RXN      PL901      -3.56            #from UbQ

PROTON   PL9-1      0
PKA      PL9-1      0.0       
ELECTRON PL9-1      1
EM       PL9-1      -145             #from UbQ
RXN      PL9-1      -18.10           #from UbQ

